diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 8c694455c121a4072b138634569f2658156a1c78..1a63e6a293424d49c51868587cbe691e847d8ae7 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -29,10 +29,10 @@ installed them, please install them now! Where appropriate the minimally
required version is given in parentheses.
* `CMake <http://cmake.org>`_ (2.6.4)
-* `Eigen3 <http://eigen.tuxfamily.org>`_ (3.2.0)
-* `Boost <http://boost.org>`_ (1.53)
-* `libpng <http://www.libpng.org>`_
* `Python2 <http://python.org>`_ (2.7)
+* `Boost <http://boost.org>`_ (1.53)
+* `zlib <https://zlib.net/>`_ (usually comes with Boost or system)
+* `Eigen3 <http://eigen.tuxfamily.org>`_ (3.2.0)
When you enable support for image processing, you will need:
@@ -40,8 +40,8 @@ When you enable support for image processing, you will need:
precision and thus also requires FFTW to be compiled with single precision.
Most platforms offer this as a second package. If you are compiling manually,
use the `--enable-single` option.
-
* `libtiff <http://www.libtiff.org>`_
+* `libpng <http://www.libpng.org>`_ (also needed for GUI)
If you would like to use the info module, also install:
@@ -157,12 +157,12 @@ short description of how CMake figures out what dependencies to take and how you
can influence it.
* Boost is mainly controlled via the `BOOST_ROOT` option. If boost wasn't
- found, it should be set to the prefix of the boost installation.
+ found, it should be set to the prefix of the boost installation. If for some
+ reason, it is desirable to use the non-multithreaded boost libraries, you can
+ switch `Boost_USE_MULTITHREADED` on (it is off by default).
* `PYTHON_ROOT` is the Python equivalent of BOOST_ROOT. It should be set to
the prefix path containing the python binary, headers and libraries.
- If the Python library (file name starting with `libpython`) is not located in
- `$PYTHON_ROOT/lib`, you should set the full path with `PYTHON_LIBRARIES`.
* `SYS_ROOT` controls the general prefix for searching libraries and headers.
By default, it is set to `/`.
@@ -176,60 +176,103 @@ can influence it.
By default this is switched off but it is highly recommended to provide a
compound library to use all features of OpenStructure.
+* `ENABLE_GUI` controls whether to build the graphical user interface module.
+ By default, this is switched on.
+
+* `ENABLE_GFX` controls whether to build the graphics module. By default, this
+ is switched on. If it is switched off, it also switches `ENABLE_GUI` off.
+
+* `ENABLE_INFO` controls whether to build the info module. By default, this is
+ switched on. If it is switched off, it also switches `ENABLE_GFX` off and
+ removes all dependencies to Qt.
+
* `QT_QMAKE_EXECUTABLE` defines the exact Qt installation to take. It should
be set to the full path to `qmake`. This is only needed if `ENABLE_INFO` is
switched on.
* `COMPILE_TMTOOLS` will activate bindings for TMAlign and TMScore, which are
then available at python level. This option requires a Fortran compiler.
- By default this option is switched off.
+ By default, this option is switched off.
* `USE_NUMPY` allows OpenStructure to pass back data in NumPy format. By
- default this is switched off.
+ default, this is switched off.
-* The paths to your local OpenMM installation are set by:
+* `ENABLE_IMG` controls whether to build the image processing module. This will
+ enable support for density maps, and general image processing in 1, 2 an 3
+ dimensions. By default, this is switched on.
+
+* `ENABLE_MM` controls whether the molecular mechanics module is enabled. By
+ default, this is switched off. If it is turned on, you should also set the
+ paths to your local OpenMM installation:
* `OPEN_MM_INCLUDE_DIR`: the include path
* `OPEN_MM_LIBRARY`: the libOpenMM library
* `OPEN_MM_PLUGIN_DIR`: the path for OpenMM plugins
* see example below for commonly used paths
+* Several paths to other libraries can be set if they are not in the expected
+ locations:
+
+ * `PYTHON_LIBRARIES` defines the location of the Python library (file name
+ starting with `libpython`). This must be set if it is not in
+ `$PYTHON_ROOT/lib`.
+ * `EIGEN3_INCLUDE_DIR` defines the include folder of Eigen3 (contains `Eigen`
+ folder with include files).
+ * `FFTW_LIBRARY` defines the location of the FFTW3 library (file name starting
+ with `libfftw3f` (or `libfftw3` if `USE_DOUBLE_PRECISION` is switched on))
+ * `FFTW_INCLUDE_DIR` defines the include folder of FFTW3 (contains include
+ files directly)
+ * `PNG_LIBRARY` defines the location of the libpng library (file name starting
+ with `libpng`)
+ * `PNG_INCLUDE_DIR` defines the include folder of libpng (contains include
+ files directly)
+ * `ZLIB_LIBRARY` defines the location of the zlib library (file name starting
+ with `libz`)
+ * `ZLIB_INCLUDE_DIR` defines the include folder of zlib (contains include
+ files directly)
+ * `TIFF_LIBRARY` defines the location of the libtiff library (file name
+ starting with `libtiff`)
+ * `TIFF_INCLUDE_DIR` defines the include folder of libtiff (contains include
+ files directly)
+ * Usually, you will receive errors for those variables when executing `cmake`
+ and set them accordingly as needed.
+
Build Options
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-* `OPTIMIZE` can be set to 1 to build an optimized (-O3 -DNDEBUG) version of
- OpenStructure.
-
-* `PREFIX` specifies the location on the file system where to install
- OpenStructure.
+* `OPTIMIZE` can be switched on to build an optimized (-O3 -DNDEBUG) version of
+ OpenStructure. By default, this is switched off.
* `USE_DOUBLE_PRECISION` will switch on double precision within OpenStructure.
By default, this is switched off.
* `ENABLE_STATIC` allows some parts of OpenStructure to be statically linked
and thus can be used more easily across a heterogeneous setup, e.g. older
- systems and newer systems.
-
-* `ENABLE_IMG` controls whether to build the image processing module. This will
- enable support for density maps, and general image processing in 1, 2 an 3
- dimensions. By default, this is switched on.
-
-* `ENABLE_MM` controls whether the molecular mechanics module is enabled. By
- default, this is switched off. If it is turned on, you should also set the
- `OPEN_MM_INCLUDE_DIR`, `OPEN_MM_LIBRARY` and `OPEN_MM_PLUGIN_DIR` flags.
+ systems and newer systems. By default, this is switched off.
-* `ENABLE_GUI` controls whether to build the graphical user interface module.
- By default, this is switched on.
+* For deployment of OpenStructure with `make install` there are two relevant
+ settings to consider:
-* `ENABLE_GFX` controls whether to build the graphics module. By default, this
- is switched on. If it is switched off, it also switches `ENABLE_GUI` off.
+ * `PREFIX` or `CMAKE_INSTALL_PREFIX` are used to define the path where the
+ OpenStructure `stage` folder will be installed to.
+ * `USE_RPATH` can be switched on to embed rpath upon make install. By default,
+ this option is switched off.
-* `ENABLE_INFO` controls whether to build the info module. By default, this is
- switched on. If it is switched off, it also switches `ENABLE_GFX` off and
- hence removes all dependencies to Qt.
+* Experimental settings (only change if you know what you are doing):
-* `USE_SHADER` controls shader support. By default, no shaders are used.
+ * `USE_MESA` to use software rendered Mesa instead of hardware GL. By default,
+ this is turned off.
+ * `USE_SHADER` controls whether to compile with shader support. By default,
+ this is turned off.
+ * `ENABLE_SPNAV` controls whether 3DConnexion devices should be supported. By
+ default, this is turned off.
+ * `PROFILE` can be switched on to enable a (very verbose) code profiler. By
+ default, this is turned off.
+ * `UBUNTU_LAYOUT` can be turned on to switch the directory layout of the
+ `stage` folder to be more ubuntu-like. By default, this is switched off.
+ * `HIDDEN_VISIBILITY` can be turned on to add "-fvisibility=hidden" to gcc's
+ compile flags (only if GNU compiler used). By default, this is switched off.
Example Configurations
@@ -243,7 +286,7 @@ follows:
.. code-block:: bash
- cmake . -DOPTIMIZE=1 -DENABLE_INFO=OFF
+ cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF
The molecular mechanics module can be enabled by installing OpenMM and adding
the appropriate flags as follows (replace `<OPENMM>` with the actual path to
@@ -251,7 +294,7 @@ OpenMM):
.. code-block:: bash
- cmake . -DOPTIMIZE=1 -DENABLE_INFO=OFF -DENABLE_MM=1 \
+ cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF -DENABLE_MM=ON \
-DOPEN_MM_LIBRARY=<OPENMM>/lib/libOpenMM.so \
-DOPEN_MM_INCLUDE_DIR=<OPENMM>/include/ \
-DOPEN_MM_PLUGIN_DIR=<OPENMM>/lib/plugins
@@ -271,7 +314,7 @@ required to use the C++98 standard:
.. code-block:: bash
- cmake . -DOPTIMIZE=1 -DENABLE_INFO=OFF -DCMAKE_CXX_FLAGS='-std=c++98'
+ cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF -DCMAKE_CXX_FLAGS='-std=c++98'
We hope to support Qt5 and C++11 in the next OpenStructure release.
@@ -295,7 +338,7 @@ version of OpenStructure.
.. code-block:: bash
cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
- -DOPTIMIZE=1
+ -DOPTIMIZE=ON
**Fedora 26 without GUI**
@@ -312,7 +355,7 @@ Qt4, the GUI and add the extra flag described above:
.. code-block:: bash
- cmake . -DOPTIMIZE=1 -DENABLE_INFO=OFF -DCMAKE_CXX_FLAGS='-std=c++98'
+ cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF -DCMAKE_CXX_FLAGS='-std=c++98'
**macOS with Homebrew without GUI**
@@ -329,7 +372,7 @@ located as they are on linux and hence they must be specified too:
cmake . -DPYTHON_INCLUDE_PATH=/usr/local/opt/python/Frameworks/Python.framework/Headers \
-DPYTHON_LIBRARIES=/usr/local/opt/python/Frameworks/Python.framework/Python \
-DBOOST_ROOT=/usr/local -DPYTHON_ROOT=/usr/local \
- -DSYS_ROOT=/usr/local -DENABLE_INFO=OFF -DOPTIMIZE=1
+ -DSYS_ROOT=/usr/local -DENABLE_INFO=OFF -DOPTIMIZE=ON
Building the Project